2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertFalse;
25 import static org.testng.AssertJUnit.assertNotNull;
26 import static org.testng.AssertJUnit.assertNull;
27 import static org.testng.AssertJUnit.assertTrue;
29 import jalview.api.FeatureRenderer;
30 import jalview.datamodel.Alignment;
31 import jalview.datamodel.AlignmentI;
32 import jalview.datamodel.SequenceDummy;
33 import jalview.datamodel.SequenceFeature;
34 import jalview.datamodel.SequenceI;
35 import jalview.gui.AlignFrame;
36 import jalview.schemes.AnnotationColourGradient;
37 import jalview.schemes.GraduatedColor;
39 import java.awt.Color;
41 import java.io.IOException;
44 import org.testng.annotations.Test;
46 public class FeaturesFileTest
49 private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
51 @Test(groups = { "Functional" })
52 public void testParse() throws Exception
54 File f = new File("examples/uniref50.fa");
55 AlignmentI al = readAlignmentFile(f);
56 AlignFrame af = new AlignFrame(al, 500, 500);
57 Map<String, Object> colours = af.getFeatureRenderer()
59 FeaturesFile featuresFile = new FeaturesFile(
60 "examples/exampleFeatures.txt", FormatAdapter.FILE);
61 assertTrue("Test " + "Features file test"
62 + "\nFailed to parse features file.",
63 featuresFile.parse(al.getDataset(), colours, true));
66 * Refetch the colour map from the FeatureRenderer (to confirm it has been
67 * updated - JAL-1904), and verify (some) feature group colours
69 colours = af.getFeatureRenderer().getFeatureColours();
70 assertEquals("26 feature group colours not found", 26, colours.size());
71 assertEquals(colours.get("Cath"), new Color(0x93b1d1));
72 assertEquals(colours.get("ASX-MOTIF"), new Color(0x6addbb));
75 * verify (some) features on sequences
77 SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
78 .getSequenceFeatures(); // FER_CAPAA
79 assertEquals(7, sfs.length);
80 SequenceFeature sf = sfs[0];
81 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
82 assertEquals(39, sf.begin);
83 assertEquals(39, sf.end);
84 assertEquals("uniprot", sf.featureGroup);
85 assertEquals("METAL", sf.type);
87 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
88 assertEquals(44, sf.begin);
89 assertEquals(44, sf.end);
90 assertEquals("uniprot", sf.featureGroup);
91 assertEquals("METAL", sf.type);
93 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
94 assertEquals(47, sf.begin);
95 assertEquals(47, sf.end);
96 assertEquals("uniprot", sf.featureGroup);
97 assertEquals("METAL", sf.type);
99 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
100 assertEquals(77, sf.begin);
101 assertEquals(77, sf.end);
102 assertEquals("uniprot", sf.featureGroup);
103 assertEquals("METAL", sf.type);
105 assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
107 assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
108 sf.links.get(0).toString());
109 assertEquals(8, sf.begin);
110 assertEquals(83, sf.end);
111 assertEquals("uniprot", sf.featureGroup);
112 assertEquals("Pfam", sf.type);
114 assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
115 assertEquals(3, sf.begin);
116 assertEquals(93, sf.end);
117 assertEquals("uniprot", sf.featureGroup);
118 assertEquals("Cath", sf.type);
121 "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
124 "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&service=NetPhos-2.0",
125 sf.links.get(0).toString());
126 assertEquals(89, sf.begin);
127 assertEquals(89, sf.end);
128 assertEquals("netphos", sf.featureGroup);
129 assertEquals("PHOSPHORYLATION (T)", sf.type);
133 * Test parsing a features file with a mix of Jalview and GFF formatted
138 @Test(groups = { "Functional" })
139 public void testParse_mixedJalviewGff() throws Exception
141 File f = new File("examples/uniref50.fa");
142 AlignmentI al = readAlignmentFile(f);
143 AlignFrame af = new AlignFrame(al, 500, 500);
144 Map<String, Object> colours = af.getFeatureRenderer()
145 .getFeatureColours();
146 // GFF2 uses space as name/value separator in column 9
147 String gffData = "METAL\tcc9900\n" + "GFF\n"
148 + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
149 + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
150 FeaturesFile featuresFile = new FeaturesFile(gffData,
151 FormatAdapter.PASTE);
152 assertTrue("Failed to parse features file",
153 featuresFile.parse(al.getDataset(), colours, true));
155 // verify colours read or synthesized
156 colours = af.getFeatureRenderer().getFeatureColours();
157 assertEquals("1 feature group colours not found", 1, colours.size());
158 assertEquals(colours.get("METAL"), new Color(0xcc9900));
160 // verify feature on FER_CAPAA
161 SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
162 .getSequenceFeatures();
163 assertEquals(1, sfs.length);
164 SequenceFeature sf = sfs[0];
165 assertEquals("Iron-sulfur,2Fe-2S", sf.description);
166 assertEquals(44, sf.begin);
167 assertEquals(45, sf.end);
168 assertEquals("uniprot", sf.featureGroup);
169 assertEquals("METAL", sf.type);
170 assertEquals(4f, sf.getScore(), 0.001f);
172 // verify feature on FER1_SOLLC
173 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
174 assertEquals(1, sfs.length);
176 assertEquals("uniprot", sf.description);
177 assertEquals(55, sf.begin);
178 assertEquals(130, sf.end);
179 assertEquals("uniprot", sf.featureGroup);
180 assertEquals("Pfam", sf.type);
181 assertEquals(2f, sf.getScore(), 0.001f);
184 public static AlignmentI readAlignmentFile(File f) throws IOException
186 System.out.println("Reading file: " + f);
187 String ff = f.getPath();
188 FormatAdapter rf = new FormatAdapter();
190 AlignmentI al = rf.readFile(ff, FormatAdapter.FILE,
191 new IdentifyFile().identify(ff, FormatAdapter.FILE));
193 al.setDataset(null); // creates dataset sequences
194 assertNotNull("Couldn't read supplied alignment data.", al);
199 * Test various ways of describing a feature colour scheme
203 @Test(groups = { "Functional" })
204 public void testParseGraduatedColourScheme() throws Exception
206 FeaturesFile ff = new FeaturesFile();
209 GraduatedColor gc = ff.parseGraduatedColourScheme(
210 "BETA-TURN-IR\t9a6a94", "label");
211 assertTrue(gc.isColourByLabel());
212 assertEquals(Color.white, gc.getMinColor());
213 assertEquals(Color.black, gc.getMaxColor());
214 assertTrue(gc.isAutoScale());
216 // using colour name, rgb, etc:
217 String spec = "blue|255,0,255|absolute|20.0|95.0|below|66.0";
218 gc = ff.parseGraduatedColourScheme("BETA-TURN-IR\t" + spec, spec);
219 assertFalse(gc.isColourByLabel());
220 assertEquals(Color.blue, gc.getMinColor());
221 assertEquals(new Color(255, 0, 255), gc.getMaxColor());
222 assertFalse(gc.isAutoScale());
223 assertFalse(gc.getTolow());
224 assertEquals(20.0f, gc.getMin(), 0.001f);
225 assertEquals(95.0f, gc.getMax(), 0.001f);
226 assertEquals(AnnotationColourGradient.BELOW_THRESHOLD,
228 assertEquals(66.0f, gc.getThresh(), 0.001f);
230 // inverse gradient high to low:
231 spec = "blue|255,0,255|95.0|20.0|below|66.0";
232 gc = ff.parseGraduatedColourScheme("BETA-TURN-IR\t" + spec, spec);
233 assertTrue(gc.isAutoScale());
234 assertTrue(gc.getTolow());
238 * Test parsing a features file with GFF formatted content only
242 @Test(groups = { "Functional" })
243 public void testParse_pureGff3() throws Exception
245 File f = new File("examples/uniref50.fa");
246 AlignmentI al = readAlignmentFile(f);
247 AlignFrame af = new AlignFrame(al, 500, 500);
248 Map<String, Object> colours = af.getFeatureRenderer()
249 .getFeatureColours();
250 // GFF3 uses '=' separator for name/value pairs in colum 9
251 String gffData = "##gff-version 3\n"
252 + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
253 + "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465\n"
254 + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
255 FeaturesFile featuresFile = new FeaturesFile(gffData,
256 FormatAdapter.PASTE);
257 assertTrue("Failed to parse features file",
258 featuresFile.parse(al.getDataset(), colours, true));
260 // verify feature on FER_CAPAA
261 SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
262 .getSequenceFeatures();
263 assertEquals(1, sfs.length);
264 SequenceFeature sf = sfs[0];
265 // description parsed from Note attribute
266 assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description);
267 assertEquals(39, sf.begin);
268 assertEquals(39, sf.end);
269 assertEquals("uniprot", sf.featureGroup);
270 assertEquals("METAL", sf.type);
272 "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465",
273 sf.getValue("ATTRIBUTES"));
275 // verify feature on FER1_SOLLC1
276 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
277 assertEquals(1, sfs.length);
279 // ID used for description if available
280 assertEquals("$23", sf.description);
281 assertEquals(55, sf.begin);
282 assertEquals(130, sf.end);
283 assertEquals("uniprot", sf.featureGroup);
284 assertEquals("Pfam", sf.type);
285 assertEquals(3f, sf.getScore(), 0.001f);
289 * Test parsing a features file with Jalview format features (but no colour
290 * descriptors or startgroup to give the hint not to parse as GFF)
294 @Test(groups = { "Functional" })
295 public void testParse_jalviewFeaturesOnly() throws Exception
297 File f = new File("examples/uniref50.fa");
298 AlignmentI al = readAlignmentFile(f);
299 AlignFrame af = new AlignFrame(al, 500, 500);
300 Map<String, Object> colours = af.getFeatureRenderer()
301 .getFeatureColours();
304 * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
306 String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
307 + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
308 FeaturesFile featuresFile = new FeaturesFile(featureData,
309 FormatAdapter.PASTE);
310 assertTrue("Failed to parse features file",
311 featuresFile.parse(al.getDataset(), colours, true));
313 // verify FER_CAPAA feature
314 SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
315 .getSequenceFeatures();
316 assertEquals(1, sfs.length);
317 SequenceFeature sf = sfs[0];
318 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
319 assertEquals(39, sf.begin);
320 assertEquals(39, sf.end);
321 assertEquals("METAL", sf.type);
323 // verify FER1_SOLLC feature
324 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
325 assertEquals(1, sfs.length);
327 assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
328 assertEquals(86, sf.begin);
329 assertEquals(87, sf.end);
330 assertEquals("METALLIC", sf.type);
333 private void checkDatasetfromSimpleGff3(AlignmentI dataset)
335 assertEquals("no sequences extracted from GFF3 file", 2,
336 dataset.getHeight());
338 SequenceI seq1 = dataset.findName("seq1");
339 SequenceI seq2 = dataset.findName("seq2");
343 "Failed to replace dummy seq1 with real sequence",
344 seq1 instanceof SequenceDummy
345 && ((SequenceDummy) seq1).isDummy());
347 "Failed to replace dummy seq2 with real sequence",
348 seq2 instanceof SequenceDummy
349 && ((SequenceDummy) seq2).isDummy());
350 String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
351 assertFalse("dummy replacement buggy for seq1",
352 placeholderseq.equals(seq1.getSequenceAsString()));
353 assertFalse("dummy replacement buggy for seq2",
354 placeholderseq.equals(seq2.getSequenceAsString()));
355 assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
356 assertEquals("Wrong number of features", 3,
357 seq1.getSequenceFeatures().length);
358 assertNull(seq2.getSequenceFeatures());
360 "Wrong number of features",
362 seq2.getSequenceFeatures() == null ? 0 : seq2
363 .getSequenceFeatures().length);
365 "Expected at least one CDNA/Protein mapping for seq1",
366 dataset.getCodonFrame(seq1) != null
367 && dataset.getCodonFrame(seq1).size() > 0);
371 @Test(groups = { "Functional" })
372 public void readGff3File() throws IOException
374 FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
376 Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
377 gffreader.addProperties(dataset);
378 checkDatasetfromSimpleGff3(dataset);
381 @Test(groups = { "Functional" })
382 public void simpleGff3FileClass() throws IOException
384 AlignmentI dataset = new Alignment(new SequenceI[] {});
385 FeaturesFile ffile = new FeaturesFile(simpleGffFile,
388 boolean parseResult = ffile.parse(dataset, null, false, false);
389 assertTrue("return result should be true", parseResult);
390 checkDatasetfromSimpleGff3(dataset);
393 @Test(groups = { "Functional" })
394 public void simpleGff3FileLoader() throws IOException
396 AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
397 simpleGffFile, FormatAdapter.FILE);
399 "Didn't read the alignment into an alignframe from Gff3 File",
401 checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
404 @Test(groups = { "Functional" })
405 public void simpleGff3RelaxedIdMatching() throws IOException
407 AlignmentI dataset = new Alignment(new SequenceI[] {});
408 FeaturesFile ffile = new FeaturesFile(simpleGffFile,
411 boolean parseResult = ffile.parse(dataset, null, false, true);
412 assertTrue("return result (relaxedID matching) should be true",
414 checkDatasetfromSimpleGff3(dataset);
417 @Test(groups = { "Functional" })
418 public void testPrintJalviewFormat() throws Exception
420 File f = new File("examples/uniref50.fa");
421 AlignmentI al = readAlignmentFile(f);
422 AlignFrame af = new AlignFrame(al, 500, 500);
423 Map<String, Object> colours = af.getFeatureRenderer()
424 .getFeatureColours();
425 String features = "METAL\tcc9900\n"
426 + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
428 + "STARTGROUP\tuniprot\n"
429 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
430 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
431 + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
432 + "ENDGROUP\tuniprot\n";
433 FeaturesFile featuresFile = new FeaturesFile(features,
434 FormatAdapter.PASTE);
435 featuresFile.parse(al.getDataset(), colours, false);
438 * first with no features displayed
440 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
441 Map<String, Object> visible = fr
442 .getDisplayedFeatureCols();
443 String exported = featuresFile.printJalviewFormat(
444 al.getSequencesArray(), visible);
445 String expected = "No Features Visible";
446 assertEquals(expected, exported);
449 * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
451 fr.setVisible("METAL");
452 fr.setVisible("GAMMA-TURN");
453 visible = fr.getDisplayedFeatureCols();
454 exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
456 expected = "METAL\tcc9900\n"
457 + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
458 + "\nSTARTGROUP\tuniprot\n"
459 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
460 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
461 + "ENDGROUP\tuniprot\n";
462 assertEquals(expected, exported);
465 * now set Pfam visible
467 fr.setVisible("Pfam");
468 visible = fr.getDisplayedFeatureCols();
469 exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
472 * note the order of feature types is uncontrolled - derives from
473 * FeaturesDisplayed.featuresDisplayed which is a HashSet
475 expected = "METAL\tcc9900\n"
477 + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
478 + "\nSTARTGROUP\tuniprot\n"
479 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
480 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
481 + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\t0.0\n"
482 + "ENDGROUP\tuniprot\n";
483 assertEquals(expected, exported);